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   <title>Doing stereospecific assignments</title>
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<h1>
Various corrections of restraint files</h1>

<h2>
Doing stereospecific assignments</h2>

<hr>
<p><b>Requirements</b>
<br>You can correct the stereospecific assignments of a AQUA formated file:
NAME.noe
<br>using the assignments given in the stereospecific assignment (ssa)
file: NAME_ass_NAME.ass (or use this <a href="brsv_ass_brsv.ass">example</a>
).
<br>You also need a pdb file containing (at least) 1 model called: NAME.pdb
<p>The following are pseudo-atom corrections in &Aring; that will be added
to any un-assigned (pro-)chiral groups are:
<br>&nbsp;
<table BORDER CELLSPACING=0 CELLPADDING=10 >
<tr>
<td>CH2/NH2</td>

<td>0.9</td>
</tr>

<tr>
<td>Aromat with 2 H</td>

<td>2.2</td>
</tr>

<tr>
<td>double NH2</td>

<td>1.5</td>
</tr>

<tr>
<td>double methyl</td>

<td>1.6</td>
</tr>
</table>

<p>The correction is actually the distance from one atom(-group) to the
pseudo atom. This can't be changed in the current setup.
<p>Type at unix level (replacing NAME with an other name):
<br>&nbsp;
<table BORDER CELLSPACING=0 CELLPADDING=10 >
<tr>
<td><b>Commands</b></td>

<td><b>Explanation</b></td>
</tr>

<tr>
<td>aqua</td>

<td>Initializes the AQUA program</td>
</tr>

<tr>
<td>assignchk NAME.pdb</td>

<td>Preperative step to generate a template stereospecific assignment (ssa)
file called: AssignDAT-new. Rename this ssa file to NAME_ass_NAME.ass (yes,
the name sucks!) or get the <a href="brsv_ass_brsv.ass">example</a>.</td>
</tr>

<tr>
<td>[your editor] NAME_ass_NAME.ass</td>

<td>Edit the last column in this file. A question mark means it will not
be stereospecifically assigned but will be turned into a pseudo atom. Changing
it to T for True means the nomenclature will be kept. Changing it to F
for False means it will be swapped. Don't forget to update the two count
items in the header.</td>
</tr>

<tr>
<td>echo "set ass f" > assign.cmm</td>

<td>The file: assign.cmm will now contain a line saying: "set ass f". This
file is read by assignchk. It means the assignment check will not propose
new assignments but will take those specified in the ssa file.</td>
</tr>

<tr>
<td>assignchk -readass NAME NAME.pdb</td>

<td>Re- and deassigns the stereospecific assignments. The file assigned.noe
contains the resulting noe restraint list in AQUA format and nomenclature.</td>
</tr>
</table>

<p>For more detailed info on assignchk, please type:
<br>qhelp <a href="../doc/assignchk.txt">assignchkw</a>
<p>For more detailed info on qassign, please type:
<br>qhelp [<a href="../doc/AquaAssign.txt">qassign</a> | <a href="../doc/assign_output.txt">assign_output</a>
| <a href="../doc/assign_method.txt">assign_method</a>]&nbsp;
<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> 
for help, when required.
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